MolNFT v1 · #114146 · protein
Homo-dimeric structure of cytochrome C' from thermophilic hydrogenophilus thermoluteolus
5B3I · Cytochrome C prime: “Homo-dimeric structure of cytochrome C' from thermophilic hydrogenophilus thermoluteolus”. X-ray diffraction, 1 ligand (HEC), 8 pockets (best druggability 0.79). MolNFT v1 #114146 on GenesisL1: 3D structure…
- PDB
- 5B3I
- Type
- protein
- Length
- 540 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C prime
- UniProt
- F7J213
- Ligands
- HEC
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 73% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Cytochrome C prime | protein | 135 | 73% helix, 3% strand | F7J213 |
Ligands and binding sites
- HEC · Heme C · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 795 | 0.79 | 0.82 | 77 | HEC |
| 2 | 442 | 0.76 | 0.85 | 51 | HEC |
| 3 | 421 | 0.72 | 0.82 | 43 | HEC |
| 4 | 422 | 0.72 | 0.82 | 45 | HEC |
| 5 | 165 | 0.45 | 0.75 | 23 | empty |
Interfaces
5 interfaces between chains.
- A–B · 965 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 946 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 326 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 25 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 16 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor (heme c attachment).
Compared structures
- 5B3I · Homo-dimeric structure of cytochrome c' from Thermophilic Hydrogenophilus thermoluteolus · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt F7J213
- Elsewhere: RCSB PDB 5B3I · PDBe 5B3I · UniProt F7J213
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